Credits
About This Project
This rhinovirus serotype surveillance dashboard provides detailed monitoring of rhinovirus genetic diversity across multiple cities through deep sequencing analysis of municipal wastewater samples generously provided by community partners. We hope to reach 75 sewersheds in the next year, so if you know other communities who might like to participate and make wastewater sequencing results public, please let Dave O'Connor (dhoconno@wisc.edu) or Marc Johnson (marcjohnson@missouri.edu; @solidevidence on Twitter and BlueSky) know. Key contributors from Marc's lab include Clayton Rushford, Alejandro Tovar-Mendez, and Devon Gregory. Nick Minor and Will Gardner in Dave's lab are responsible for data analysis and visualization. NVD is performed using UW-Madison Center for High Throughput Computing resources.
Collaborators
- Nucleic Acid Observatory, SecureBio: SecureBio SecureBio funds most sequencing flow cells through their sponsor, Open Philanthropy.
- Rachel Poretsky, University of Illinois, Chicago: Poretskly lab
- Jason Rothman, University of California, Riverside: Jason Rothman
Community partners
Visualization Explanation
Rhinovirus Serotype Activity Timeline
This interactive visualization displays when different rhinovirus serotypes are detected across cities over time. Each row represents a specific rhinovirus serotype (e.g., rhinovirus A1, rhinovirus C42), and time progresses from left to right.
Reading the Plot:
- Circles: Each circle represents detection of a serotype in a city on a specific date
- Circle Size: Larger circles indicate higher viral abundance (shown as reads per billion)
- Circle Color: Different colors represent different cities/sewersheds
- Timeline: X-axis shows sample collection dates with a scrollable timeline. Note that not all sewersheds have data over the full time period.
- Serotype Order: Y-axis lists serotypes ordered by the first timepoint when a serotype is detected for four consecutive weeks. Serotypes that haven't been detected for at least four consecutive weeks are not shown.
Interactive Controls:
- Timeline Slider: Use the bottom slider to zoom in/out on specific time periods
- City Legend: Click city names to toggle visibility on/off; double-click to isolate a single city
- Hover Details: Hover over circles to see exact dates, serotype names, and abundance values
Symbol Calculations:
- Reads Per Billion (RPB): Viral abundance is calculated as the number of sequencing reads matching each serotype divided by the total number of reads in the sample, multiplied by one billion for easier interpretation
- Detection Threshold: Only serotypes with RPB > 0.1 are displayed
- Circle Sizing: Circle diameter is proportional to the square root of RPB values to make differences more visually apparent while preventing extreme outliers from dominating the display
Data & Analysis
- Data Collection: Wastewater samples are collected from designated sewersheds and sent to Marc Johnson's laboratory at the University of Missouri for processing. The laboratory employs a multi-step process to prepare the samples for analysis. First, samples are filtered through a 0.22 um filter to remove bacteria and other solids. Samples are then mixed with polyethylene glycol (PEG) and precipitated to concentrate viruses from the wastewater samples. This step is crucial as viral particles are typically present in low concentrations in raw wastewater, so sequencing from wastewater without enrichment can miss viral sequences. Following precipitation, total nucleic acids are extracted from the virus-enriched samples. The extracted nucleic acids then undergo library preparation to make them compatible with next-generation sequencing technology. Finally, the prepared libraries are sequenced on an Illumina NovaSeq instrument at the University of Missouri, generating billions of short reads that represent the genetic material present in the sample.
- Rhinovirus Analysis Pipeline: The raw sequencing data is processed through a metagenomic analysis pipeline, NVD, developed by Dave O'Connor to identify viral sequences. This pipeline was developed specifically for identifying and exploring metagenomes for families of viruses that infect humans (and often animals). NVD results are stored on a Labkey Server SDMS. Results from sites that have agreed to have their data made public are retrieved from Labkey, analyzed for serotype patterns, and visualized. The data used for these plots is available as an Excel file.
- Update Frequency: Wastewater samples are delivered to Marc Johnson's lab weekly. It typically takes two to three weeks for nucleic acids to be isolated, sequenced, analyzed, and available for inclusion in the dashboards. The dashboards themselves update automatically each night.
Data Usage & Licensing
This data provided here is intended for public use and is made available under a CC BY-NC-SA 4.0 license that allows unrestricted sharing and adapting for non-commercial use.
Disclaimer
The raw data published on this dashboard has been obtained from deidentified and aggregated materials collected in accordance with the law and ethical guidelines governing the research studies. This data is made available for informational purposes only. This data set has not been independently verified, validated, or peer reviewed. It may contain errors, omissions, or artifacts inherent to the methods used in data collection and processing and is provided as is without any warranty of accuracy or completeness.
This data is neither intended for clinical or diagnostic purposes nor should it be used for making public policy. Users must not rely on this dataset to inform health care decisions, public health strategies, or regulatory actions. Any conclusions drawn from this data are the sole responsibility of the user.
By accessing or using this data, you assume all risks and acknowledge these limitations. You further agree to use this data responsibly, in compliance with all applicable legal and ethical standards.
About Lungfish
Lungfish is a project funded by Inkfish Medical. Dave O'Connor, Shelby O'Connor, and Marc Johnson jointly lead the Lungfish project from their labs at the University of Wisconsin-Madison and University of Missouri.